Did you try synchronizing (looking at your trophy card before signing off on the PS3) or doing a hard refresh (Ctrl+f5) after updating the card? It could also just be your gamer card's server that might be a little slow.
I'm having the exact same problem ... currently I'm playing AC: Revelations and my Gamer Card isn't going up with my trophy count anymore either.
I've tried your suggestions and nothing seems to work ... I had this same problem with 007 Blood Stone - it took about a year (or more) for my Gamer Card to catch up.